Fig. 2

Example ChIPs applications. a–d Evaluation of the effects of varying experimental parameters on peak calling performance. Results are based on simulation of generic TF and HM datasets for chr21 as described in Additional file 1: Supplementary Methods. In each plot the y-axis shows the F1 score computed by comparing ground truth peaks to those inferred from simulated datasets using MACS2. a F1 score as a function of the total number of reads simulated from chr21. b F1 score as a function of read length. c F1 score as a function of PCR duplicates. The x-axis gives the parameter p, which can be interpreted as the percent of fragments with no PCR duplicates (Additional file 1: Supplementary Table 2). d F1 score as a function of mean fragment length (bp). Red = HM; Blue = TF; solid lines=paired end reads; dashed lines=single end reads. e–f Evaluation of various peak calling methods on simulated TF (e) and HM (f) datasets with different noise levels. Noise levels are quantified using s, the fraction of pulled down reads that originate from true binding sites. Blue = BCP; orange = GEM; green = MACS2; red = MUSIC; purple = HOMER